A new setting in Tools > Options > Environment to go along with "Separate compiled code from new files" which tells LV to honor that global setting instead of the one applied to projects, classes, etc.
When you pull in legacy projects or other tree-type files which have the "separate compiled" option unchecked, anything new you make in them also has it unchecked even if your global setting is to separate.
I saw my father do some work on a car once as a kid and I asked him "How did you know how to do that?" He responded "I didn't, I had to figure it out."
It's better software engineering practice to modify your source with your desired settings rather than having environment settings override things.